PFRMAT SS TARGET T0163 AUTHOR 4069-6308-1312 METHOD This file is the result of combining several RDB files, specifically METHOD T0163.t2k.dssp-ebghstl.rdb (weight 1.53986) METHOD T0163.t2k.stride-ebghtl.rdb (weight 1.24869) METHOD T0163.t2k.str.rdb (weight 1.53983) METHOD T0163.t2k.alpha.rdb (weight 0.659012) METHOD These files were combined by translating their predictions into EHL METHOD predictions with tables generated by compare-real, and then combining METHOD those predictions with weights proportional to their mutual information METHOD with the EHL alphabet. The comments from the individual files follow. METHOD METHOD Comments from T0163.t2k.dssp-ebghstl.rdb METHOD ============================================ METHOD TARGET T0163 METHOD Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 5 15 METHOD 7 15 METHOD 9 15 METHOD 13 7 (1 EBGHSTL ) METHOD The input amino acid frequencies were determined from METHOD alignment T0163.t2k-thin90.a2m.gz METHOD with weighted counts, using HenikoffWeight(-1 bits/column, 1) METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 570 METHOD METHOD ============================================ METHOD Comments from T0163.t2k.stride-ebghtl.rdb METHOD ============================================ METHOD TARGET T0163 METHOD Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 5 15 METHOD 7 15 METHOD 9 15 METHOD 13 6 (1 EBGHTL ) METHOD The input amino acid frequencies were determined from METHOD alignment T0163.t2k-thin90.a2m.gz METHOD with weighted counts, using HenikoffWeight(-1 bits/column, 1) METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 570 METHOD METHOD ============================================ METHOD Comments from T0163.t2k.str.rdb METHOD ============================================ METHOD TARGET T0163 METHOD Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 5 15 METHOD 7 15 METHOD 9 15 METHOD 13 13 (1 str ) METHOD The input amino acid frequencies were determined from METHOD alignment T0163.t2k-thin90.a2m.gz METHOD with weighted counts, using HenikoffWeight(-1 bits/column, 1) METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 570 METHOD METHOD ============================================ METHOD Comments from T0163.t2k.alpha.rdb METHOD ============================================ METHOD TARGET T0163 METHOD Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net METHOD This is a 4-layer network, with METHOD window units METHOD 5 15 METHOD 7 15 METHOD 9 15 METHOD 13 11 (1 ABCDEFGHIST ) METHOD The input amino acid frequencies were determined from METHOD alignment T0163.t2k-thin90.a2m.gz METHOD with weighted counts, using HenikoffWeight(-1 bits/column, 1) METHOD Counts were regularized to probabilities using METHOD /projects/compbio/lib/recode3.20comp METHOD Total sequence weight for alignment was 570 METHOD METHOD ============================================ MODEL 1 M C 0.92 K C 0.86 R C 0.78 H C 0.78 Y C 0.71 E C 0.53 A E 0.92 V E 0.93 V E 0.93 I E 0.84 G C 0.69 G C 0.87 G C 0.68 I H 0.89 I H 0.93 G H 0.95 S H 0.96 A H 0.96 I H 0.96 A H 0.96 Y H 0.96 Y H 0.96 L H 0.95 A H 0.95 K H 0.88 E C 0.62 N C 0.94 K C 0.91 N C 0.52 T E 0.91 A E 0.93 L E 0.93 F E 0.90 E E 0.73 S C 0.66 G C 0.84 T C 0.81 M C 0.78 G C 0.79 G C 0.76 R C 0.70 T C 0.59 T C 0.52 S C 0.50 A C 0.51 A C 0.54 A C 0.57 G C 0.60 M C 0.45 L E 0.46 G C 0.56 A C 0.61 H C 0.65 A C 0.62 E C 0.66 C C 0.71 E C 0.73 E C 0.69 R C 0.66 D H 0.69 A H 0.80 F H 0.85 F H 0.87 D H 0.88 F H 0.88 A H 0.89 M H 0.92 H H 0.90 S H 0.90 Q H 0.91 R H 0.91 L H 0.90 Y H 0.90 K H 0.90 G H 0.88 L H 0.86 G H 0.82 E H 0.80 E H 0.76 L H 0.65 Y H 0.63 A H 0.56 L H 0.48 S C 0.61 G C 0.72 V C 0.69 D C 0.69 I C 0.63 R C 0.57 Q E 0.48 H E 0.48 N C 0.52 G C 0.69 G C 0.74 M E 0.52 F E 0.77 K E 0.79 L E 0.73 A E 0.53 F C 0.74 S C 0.86 E H 0.64 E H 0.71 D H 0.77 V H 0.81 L H 0.81 Q H 0.82 L H 0.81 R H 0.82 Q H 0.78 M H 0.70 D H 0.56 D C 0.58 L C 0.75 D C 0.78 S C 0.73 V C 0.59 S C 0.49 W C 0.51 Y C 0.75 S C 0.88 K H 0.90 E H 0.91 E H 0.90 V H 0.90 L H 0.84 E H 0.72 K H 0.58 E C 0.63 P C 0.65 Y C 0.67 A C 0.71 S C 0.78 G C 0.72 D C 0.71 I C 0.56 F C 0.45 G E 0.52 A E 0.61 S E 0.67 F E 0.67 I C 0.51 Q C 0.70 D C 0.78 D C 0.70 V C 0.60 H E 0.48 V C 0.52 E C 0.80 P H 0.85 Y H 0.93 F H 0.94 V H 0.94 C H 0.95 K H 0.96 A H 0.96 Y H 0.96 V H 0.96 K H 0.96 A H 0.96 A H 0.96 K H 0.94 M H 0.88 L C 0.71 G C 0.94 A C 0.86 E E 0.76 I E 0.83 F E 0.77 E E 0.50 H C 0.78 T C 0.74 P E 0.55 V E 0.79 L E 0.81 H E 0.86 V E 0.87 E E 0.85 R E 0.74 D C 0.56 G C 0.86 E C 0.73 A E 0.77 L E 0.89 F E 0.92 I E 0.92 K E 0.91 T E 0.74 P C 0.78 S C 0.92 G C 0.78 D E 0.73 V E 0.87 W E 0.83 A E 0.79 N E 0.70 H E 0.88 V E 0.92 V E 0.92 V E 0.89 A E 0.58 S C 0.75 G C 0.83 V C 0.65 W C 0.55 S H 0.60 G H 0.71 M H 0.73 F H 0.77 F H 0.77 K H 0.75 Q H 0.72 L C 0.52 G C 0.84 L C 0.82 N C 0.82 N C 0.82 A C 0.78 F C 0.63 L C 0.56 P C 0.59 V C 0.54 K C 0.56 G C 0.49 E E 0.79 C E 0.90 L E 0.91 S E 0.90 V E 0.81 W E 0.54 N C 0.71 D C 0.82 D C 0.81 I C 0.80 P C 0.74 L C 0.67 T C 0.57 K E 0.54 T E 0.65 L E 0.66 Y C 0.60 H C 0.79 D C 0.86 H C 0.69 C E 0.67 Y E 0.87 I E 0.90 V E 0.89 P E 0.83 R E 0.48 K C 0.83 S C 0.91 G C 0.90 R E 0.51 L E 0.86 V E 0.89 V E 0.86 G E 0.69 A E 0.48 T C 0.59 M C 0.60 K C 0.60 P C 0.66 G C 0.78 D C 0.82 W C 0.81 S C 0.82 E C 0.79 T C 0.82 P C 0.85 D C 0.88 L H 0.88 G H 0.91 G H 0.92 L H 0.94 E H 0.94 S H 0.94 V H 0.94 M H 0.95 K H 0.95 K H 0.94 A H 0.94 K H 0.92 T H 0.87 M H 0.78 L H 0.51 P H 0.52 A C 0.49 I C 0.53 Q C 0.63 N C 0.63 M C 0.66 K C 0.57 V E 0.41 D E 0.51 R E 0.59 F E 0.54 W E 0.52 A E 0.46 G C 0.52 L E 0.49 R E 0.51 P C 0.60 G C 0.64 T C 0.82 K C 0.84 D C 0.87 G C 0.85 K C 0.77 P C 0.53 Y E 0.58 I E 0.55 G C 0.53 R C 0.55 H C 0.69 P C 0.77 E C 0.85 D C 0.79 S C 0.83 R C 0.82 I E 0.68 L E 0.88 F E 0.89 A E 0.83 A E 0.60 G C 0.65 H C 0.72 F C 0.79 R C 0.74 N C 0.70 G C 0.56 I H 0.51 L H 0.54 L H 0.61 A H 0.73 P H 0.93 A H 0.95 T H 0.95 G H 0.96 A H 0.96 L H 0.96 I H 0.96 S H 0.96 D H 0.96 L H 0.95 I H 0.92 M H 0.69 N C 0.73 K C 0.90 E C 0.86 V C 0.82 N C 0.78 Q C 0.61 D C 0.58 W C 0.54 L C 0.58 H C 0.65 A C 0.66 F C 0.75 R C 0.82 I C 0.51 D C 0.50 R C 0.48 K C 0.75 E C 0.83 A C 0.66 V C 0.66 Q C 0.71 I C 0.91 END